rs12819116

chr12-12493587-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_030640.3(DUSP16):c.532-6400C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 151,952 control chromosomes in the GnomAD database, including 7,577 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.30 (7577 hom., cov: 31)
• Consequence: DUSP16 NM_030640.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.298

Genes affected

DUSP16 (HGNC:17909): (dual specificity phosphatase 16) This gene encodes a mitogen-activated protein kinase phosphatase that is a member of the dual specificity protein phosphatase subfamily. These phosphatases inactivate their target kinases by dephosphorylating both the phosphoserine/threonine and phosphotyrosine residues. The encoded protein specifically regulates the c-Jun amino-terminal kinase (JNK) and extracellular signal-regulated kinase (ERK) pathways.[provided by RefSeq, May 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DUSP16	NM_030640.3	c.532-6400C>T		intron_variant		ENST00000298573.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DUSP16	ENST00000298573.9	c.532-6400C>T		intron_variant		1	NM_030640.3	P1
DUSP16	ENST00000228862.3	c.368-6400C>T		intron_variant		5
DUSP16	ENST00000545864.1	n.265-6400C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45999 AN: 151834 Hom.: 7577 Cov.: 31

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.306

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.303 AC: 46022 AN: 151952 Hom.: 7577 Cov.: 31 AF XY: 0.306 AC XY: 22753 AN XY: 74248

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.302

Alfa AF: 0.335 Hom.: 7172

Bravo AF: 0.294

Asia WGS AF: 0.171 AC: 599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.24
Dann	Benign	0.39

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12819116; hg19: chr12-12646521;